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Zinc in PDB 1s64: Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion

Enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion

All present enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion:
2.5.1.58; 2.5.1.59;

Protein crystallography data

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion, PDB code: 1s64 was solved by T.S.Reid, S.B.Long, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.153, 268.681, 184.622, 90.00, 131.55, 90.00
R / Rfree (%) 19.2 / 21.3

Other elements in 1s64:

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion also contains other interesting chemical elements:

Chlorine (Cl) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion (pdb code 1s64). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion, PDB code: 1s64:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1s64

Go back to Zinc Binding Sites List in 1s64
Zinc binding site 1 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:45.7
occ:1.00
 OD2 B:ASP269 2.0 42.9 1.0
NE2 B:HIS321 2.1 49.9 1.0
N18 B:778380 2.1 44.8 1.0
SG B:CYS271 2.3 49.1 1.0
CG B:ASP269 2.7 44.0 1.0
OD1 B:ASP269 2.7 47.7 1.0
C17 B:778380 2.9 45.4 1.0
CE1 B:HIS321 3.0 48.0 1.0
CD2 B:HIS321 3.0 46.8 1.0
CB B:CYS271 3.3 46.3 1.0
C12 B:778380 3.3 45.4 1.0
ND1 B:HIS321 4.1 46.9 1.0
CB B:ASP269 4.1 43.7 1.0
N11 B:778380 4.1 48.2 1.0
CG B:HIS321 4.1 48.5 1.0
CE B:LYS311 4.2 66.8 1.0
N B:CYS271 4.2 45.2 1.0
C7 B:778380 4.3 46.2 1.0
CB B:LYS311 4.4 56.6 1.0
CA B:CYS271 4.4 45.7 1.0
O B:HOH415 4.6 47.1 1.0
CD2 B:LEU320 4.6 42.2 1.0
NZ B:LYS311 4.7 69.2 1.0
CE2 B:TYR272 4.9 42.2 1.0

Zinc binding site 2 out of 6 in 1s64

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Zinc binding site 2 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:43.4
occ:1.00
 NE2 D:HIS321 2.0 43.3 1.0
OD2 D:ASP269 2.0 40.6 1.0
N18 D:778381 2.1 47.0 1.0
SG D:CYS271 2.3 37.1 1.0
CG D:ASP269 2.7 39.7 1.0
OD1 D:ASP269 2.7 40.1 1.0
CE1 D:HIS321 2.9 41.6 1.0
CD2 D:HIS321 3.0 42.9 1.0
C17 D:778381 3.0 45.7 1.0
C12 D:778381 3.3 46.1 1.0
CB D:CYS271 3.3 37.6 1.0
ND1 D:HIS321 4.0 41.5 1.0
CG D:HIS321 4.1 42.3 1.0
CB D:ASP269 4.1 37.8 1.0
N11 D:778381 4.1 46.7 1.0
CE D:LYS311 4.2 65.0 1.0
C7 D:778381 4.2 46.6 1.0
N D:CYS271 4.3 36.3 1.0
CB D:LYS311 4.3 55.2 1.0
CA D:CYS271 4.4 36.5 1.0
CD2 D:LEU320 4.6 41.2 1.0
O D:HOH430 4.6 44.1 1.0
NZ D:LYS311 4.7 67.2 1.0
CE2 D:TYR272 4.9 40.1 1.0

Zinc binding site 3 out of 6 in 1s64

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Zinc binding site 3 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:46.0
occ:1.00
 OD2 F:ASP269 2.0 41.5 1.0
NE2 F:HIS321 2.1 42.4 1.0
N18 F:778381 2.1 44.7 1.0
SG F:CYS271 2.3 45.8 1.0
CG F:ASP269 2.6 40.8 1.0
OD1 F:ASP269 2.7 44.8 1.0
C17 F:778381 2.9 42.1 1.0
CD2 F:HIS321 3.0 41.4 1.0
CE1 F:HIS321 3.0 41.9 1.0
CB F:CYS271 3.3 40.5 1.0
C12 F:778381 3.3 45.3 1.0
CB F:ASP269 4.0 41.2 1.0
ND1 F:HIS321 4.1 42.7 1.0
CG F:HIS321 4.1 44.1 1.0
N11 F:778381 4.1 45.0 1.0
CE F:LYS311 4.2 71.6 1.0
N F:CYS271 4.2 40.6 1.0
C7 F:778381 4.3 45.0 1.0
CA F:CYS271 4.3 40.1 1.0
CB F:LYS311 4.4 58.5 1.0
O F:HOH436 4.5 47.2 1.0
CD2 F:LEU320 4.6 46.6 1.0
NZ F:LYS311 4.7 73.5 1.0
CE2 F:TYR272 4.9 41.1 1.0

Zinc binding site 4 out of 6 in 1s64

Go back to Zinc Binding Sites List in 1s64
Zinc binding site 4 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:55.8
occ:1.00
 OD2 H:ASP269 2.0 44.0 1.0
NE2 H:HIS321 2.2 67.9 1.0
N18 H:778381 2.2 54.1 1.0
SG H:CYS271 2.2 58.9 1.0
CG H:ASP269 2.6 51.4 1.0
OD1 H:ASP269 2.7 56.5 1.0
C17 H:778381 3.0 51.4 1.0
CD2 H:HIS321 3.1 67.9 1.0
CE1 H:HIS321 3.1 66.7 1.0
CB H:CYS271 3.2 55.5 1.0
C12 H:778381 3.3 51.8 1.0
CB H:ASP269 4.0 50.9 1.0
N11 H:778381 4.1 51.9 1.0
ND1 H:HIS321 4.1 67.3 1.0
CG H:HIS321 4.2 67.0 1.0
N H:CYS271 4.2 52.1 1.0
CA H:CYS271 4.3 53.2 1.0
C7 H:778381 4.3 50.9 1.0
CE H:LYS311 4.3 83.4 1.0
O H:HOH407 4.4 58.6 1.0
CB H:LYS311 4.4 80.9 1.0
CD2 H:LEU320 4.6 58.9 1.0
CE2 H:TYR272 4.8 47.1 1.0
NZ H:LYS311 4.8 83.1 1.0

Zinc binding site 5 out of 6 in 1s64

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Zinc binding site 5 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:39.0
occ:1.00
 OD2 J:ASP269 2.0 33.3 1.0
NE2 J:HIS321 2.1 47.2 1.0
N18 J:778381 2.1 42.2 1.0
SG J:CYS271 2.3 38.7 1.0
CG J:ASP269 2.7 37.4 1.0
OD1 J:ASP269 2.7 38.8 1.0
C17 J:778381 2.9 41.2 1.0
CE1 J:HIS321 3.0 46.5 1.0
CD2 J:HIS321 3.0 45.9 1.0
CB J:CYS271 3.3 38.1 1.0
C12 J:778381 3.3 41.8 1.0
ND1 J:HIS321 4.1 43.8 1.0
CB J:ASP269 4.1 35.3 1.0
N11 J:778381 4.1 42.1 1.0
CG J:HIS321 4.1 45.4 1.0
N J:CYS271 4.2 39.4 1.0
CE J:LYS311 4.3 60.2 1.0
C7 J:778381 4.3 40.9 1.0
CA J:CYS271 4.3 38.8 1.0
CB J:LYS311 4.4 50.9 1.0
CD2 J:LEU320 4.6 39.3 1.0
O J:HOH429 4.7 45.6 1.0
NZ J:LYS311 4.8 61.4 1.0
CE2 J:TYR272 4.9 35.8 1.0

Zinc binding site 6 out of 6 in 1s64

Go back to Zinc Binding Sites List in 1s64
Zinc binding site 6 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rat Protein Geranylgeranyltransferase Type-I Complexed with L-778,123 and A Sulfate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:35.0
occ:1.00
 OD2 L:ASP269 2.0 29.8 1.0
NE2 L:HIS321 2.0 36.7 1.0
N18 L:778381 2.1 34.5 1.0
SG L:CYS271 2.2 35.6 1.0
CG L:ASP269 2.7 30.3 1.0
OD1 L:ASP269 2.8 28.1 1.0
C17 L:778381 2.9 32.7 1.0
CD2 L:HIS321 3.0 34.9 1.0
CE1 L:HIS321 3.0 35.4 1.0
CB L:CYS271 3.3 31.4 1.0
C12 L:778381 3.3 34.0 1.0
ND1 L:HIS321 4.1 35.1 1.0
N11 L:778381 4.1 34.9 1.0
CG L:HIS321 4.1 36.6 1.0
CB L:ASP269 4.1 29.7 1.0
N L:CYS271 4.2 32.7 1.0
C7 L:778381 4.2 34.7 1.0
CE L:LYS311 4.3 58.1 1.0
CA L:CYS271 4.3 30.8 1.0
CB L:LYS311 4.4 44.0 1.0
CD2 L:LEU320 4.6 36.6 1.0
O L:HOH446 4.7 31.0 1.0
NZ L:LYS311 4.8 60.9 1.0
CE2 L:TYR272 4.9 32.2 1.0

Reference:

T.S.Reid, S.B.Long, L.S.Beese. Crystallographic Analysis Reveals That Anticancer Clinical Candidate L-778,123 Inhibits Protein Farnesyltransferase and Geranylgeranyltransferase-I By Different Binding Modes. Biochemistry V. 43 9000 2004.
ISSN: ISSN 0006-2960
PubMed: 15248757
DOI: 10.1021/BI049280B
Page generated: Wed Oct 16 18:44:47 2024

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